Development of a 44K SNP assay focussing on the analysis of a varroa‐specific defence behaviour in honey bees (<i>Apis mellifera carnica</i>)

Spötter, A.; Gupta, Pooja; Nürnberg, Gerd; Reinsch, Norbert; Bienefeld, Kaspar

doi:10.1111/j.1755-0998.2011.03106.x

Cited by 50 publications

(43 citation statements)

References 39 publications

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“…The reported recombination rate of 19 cM/Mb was used [15,19]. In the base population, 44 000 marker loci [20] with the highest minor allele frequency (MAF) were chosen (the cut-off MAF was > 5%). Out of these 44 000 marker loci, 250 with the highest MAF were taken as quantitative trait loci (QTL) and the remaining as single nucleotide polymorphisms (SNP).…”

Section: Methodsmentioning

confidence: 99%

Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)

et al. 2013

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BackgroundThe honey bee is an economically important species. With a rapid decline of the honey bee population, it is necessary to implement an improved genetic evaluation methodology. In this study, we investigated the applicability of the unified approach and its impact on the accuracy of estimation of breeding values for maternally influenced traits on a simulated dataset for the honey bee. Due to the limitation to the number of individuals that can be genotyped in a honey bee population, the unified approach can be an efficient strategy to increase the genetic gain and to provide a more accurate estimation of breeding values. We calculated the accuracy of estimated breeding values for two evaluation approaches, the unified approach and the traditional pedigree based approach. We analyzed the effects of different heritabilities as well as genetic correlation between direct and maternal effects on the accuracy of estimation of direct, maternal and overall breeding values (sum of maternal and direct breeding values). The genetic and reproductive biology of the honey bee was accounted for by taking into consideration characteristics such as colony structure, uncertain paternity, overlapping generations and polyandry. In addition, we used a modified numerator relationship matrix and a realistic genome for the honey bee.ResultsFor all values of heritability and correlation, the accuracy of overall estimated breeding values increased significantly with the unified approach. The increase in accuracy was always higher for the case when there was no correlation as compared to the case where a negative correlation existed between maternal and direct effects.ConclusionsOur study shows that the unified approach is a useful methodology for genetic evaluation in honey bees, and can contribute immensely to the improvement of traits of apicultural interest such as resistance to Varroa or production and behavioural traits. In particular, the study is of great interest for cases where negative correlation between maternal and direct effects and uncertain paternity exist, thus, is of relevance for other species as well. The study also provides an important framework for simulating genomic and pedigree datasets that will prove to be helpful for future studies.

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Section: Methodsmentioning

confidence: 99%

Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)

et al. 2013

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“…A SNP is a change of a single base, While SNPs have only been used in two evolutionary studies (Whitfield et al, 2006;Zayed and Whitfield, 2008) and a QTL study (Spötter et al, 2012), they have great potential for application in subspecies identification, for several reasons. At the analytical level, the genome-wide coverage (coding and non-coding regions), ubiquity, codominance, and conformation to infinite sites model of evolution (Vignal et al, 2002) facilitate employment of more powerful and robust approaches, potentially leading to more reliable identification and more accurate estimates of introgression levels.…”

Section: Single Nucleotide Polymorphisms (Snps)mentioning

confidence: 99%

“…Otherwise, it must be developed (as in Whitfield et al, 2006 andSpötter et al, 2012), an expensive and time consuming endeavour requiring high tech equipment and expertise often only available in a core laboratory facility (see development details in Spötter et al, 2012 (Table 6). …”

Section: Single Nucleotide Polymorphisms (Snps)mentioning

confidence: 99%

Standard methods for characterising subspecies and ecotypes ofApis mellifera

Meixner

Pinto

Bouga

et al. 2013

Journal of Apicultural Research

203

195

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SummaryThe natural diversity of honey bees in Europe is eroding fast. A multitude of reasons lead to a loss of both genetic diversity and specific adaptations to local conditions. To preserve locally adapted bees through breeding efforts and to maintain regional strains in conservation areas, these valuable populations need to be identified.In this paper, we give an overview of methods that are currently available and used for recognition of honey bee subspecies and ecotypes, or that can be utilised to verify the genetic origin of colonies for breeding purposes. Beyond summarising details of morphometric, allozyme and DNA methods currently in use, we report recommendations with regard to strategies for sampling, and suggest methods for statistical data analysis. In particular, we emphasise the importance of reference data and consistency of methods between laboratories to yield comparable results. Métodos estándar para la caracterización de las subespecies y ecotipos de Apis mellifera ResumenLa diversidad natural de la abeja de la miel se está deteriorando rápidamente en Europa. Existen multitud de razones que conducen tanto a una pérdida de diversidad genética como de adaptaciones específicas a las condiciones locales. Se necesita identificar a estas valiosas poblaciones para preservar a las abejas adaptadas a nivel local, mediante esfuerzos para la mejora y el mantenimiento de variedades regionales en las áreas de conservación.En este artículo, realizamos una revisión general de los actuales métodos disponibles que se utilizan para la determinación de subespecies y ecotipos de abejas melíferas, o que pueden ser utilizados para verificar el origen genético de las colmenas seleccionadas con fines de cría.Además, resumimos las características de los métodos morfométricos, de aloenzimas y de ADN, realizamos recomendaciones con respecto a las estrategias de muestreo, y sugerimos métodos para el análisis estadístico de los datos. En particular, destacamos la importancia de los datos de referencia y la coherencia de los métodos entre laboratorios para producir resultados comparables.

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“…Besides the availability of the genome sequence several genomic and proteomic tools are available that might enhance further molecular studies of social behavior, including a microsatellite linkage map comprising 2000 markers [72], a 44K SNP array [74], a highdensity oligo-nucleotide array [2], and an organ-level protein atlas [68]. Further genome sequencing projects are underway to improve the current A. mellifera assembly, as well as the to end up the germ line.…”

Section: Box 2 the Genome Of The Honeybeementioning

confidence: 99%

Genetic underpinnings of division of labor in the honeybee (Apis mellifera)

Lattorff

Moritz

2013

Trends in Genetics

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Honeybees have been studied for centuries, starting with Aristotle, who wrote the first book about bee breeding. More than 2000 years later, the honeybee entered the genomic era as the first social insect whose genome was sequenced, leading to significant insight into the molecular mechanisms underlying social behavior. Additionally, gene expression studies and knock-down using RNAi have extended the understanding of social interactions. Much of the work has focused on caste determination -the mechanism that results in reproductive division of labor, division of labor within the worker caste, and worker reproduction -an essential process underlying eusociality.Here we review the molecular factors involved in caste determination and the differential regulation of caste-specific genes. Recent findings suggest that division of

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Development of a 44K SNP assay focussing on the analysis of a varroa‐specific defence behaviour in honey bees (Apis mellifera carnica)

Cited by 50 publications

References 39 publications

Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)

Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)

Standard methods for characterising subspecies and ecotypes ofApis mellifera

Genetic underpinnings of division of labor in the honeybee (Apis mellifera)

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